It does not matter. By fitting manually you are doing manual minimisation. The same treatment is applied. You are trying to optimise fit of the model into the electron density. I did these tests few years back and results were as expected. Independent on minimisation tools (manual, automatic, partial, full: real space, reciprocal space) exactly same "model bias" is added. As I said the reason is Parseval's theorem (with some adjustments in case when you are using maximum likelihood refinement)
Garib On 23 May 2011, at 21:45, Hailiang Zhang wrote: > Thanks Garib, but my task was not real space refinement (just manual model > building/adjustment). Following is my previous post. Thanks! > > """I am not doing real space refinement. Actually I am only using the > maps for manual model building/adjustments. In this case, if some Rfree > reflections have strong scattering intensities, removing them may lead to > featureless density maps. However, if we just leave them in, do you think > we may have the so-called model-bias issue?""" > > Hailiang > >> It should be remembered that refining in real space is equivalent to >> refinement in the reciprocal space (through Parseval's theorem). If you >> want to do consistent refinement then you need to use exactly same >> reflections for free and working set. If you do not use the same set of >> reflections for real and reciprocal space refinements then you may get >> very interesting results. >> >> Garib >> >> >> >> >> On 23 May 2011, at 21:17, Hailiang Zhang wrote: >> >>> Thanks Nat! I am not doing real space refinement. Actually I am only >>> using >>> the maps for manual model building/adjustments. In this case, if some >>> Rfree reflections have strong scattering intensities, removing them may >>> lead to featureless density maps. However, if we just leave them in, do >>> you think we may have the so-called model-bias issue? >>> >>> Hailiang >>> >>> >>>> On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang <zhan...@umbc.edu> >>>> wrote: >>>> >>>>> I have a preliminary question. I understand Rfree reflection sets are >>>>> never used during automatic refinement, but, when generating the real >>>>> space density maps, do we have to exclude Rfree columns? Any >>>>> references >>>>> will also be greatly appreciated! >>>>> >>>> >>>> If you are going to run overall real-space refinement on the structure, >>>> you >>>> should absolutely exclude the test set reflections from the map. If >>>> you >>>> are >>>> only going to run local refinement of small parts of the model in Coot >>>> or >>>> equivalent, it's debatable - in practice, I think most people/programs >>>> leave >>>> them in. >>>> >>>> -Nat >>>> >> >> >>
